1. Use:
recon-all -i MRI-image.nii -s test_subject -all
this will produce an aseg.mgz that is our segmentation. You can extract the left (17) and right (53) hippocampi using mri_extract_label. Soemthing like:
mri_extract_label aseg.mgz 17 53 hippocampi.mgz
note that we also generate hippocampal subfields with:
recon-all -s test_subejct -hippo-subfields
The answer to 2 and 3 are both "no". Sorry. Bruce
On Mon, 26 Nov 2012, Andrea Tateo wrote:
Hello,
I am working on segmentation of the hippocampus and I need a comparing method.
I am approaching for the first time to FreeSurfer method.
I would like your courteous help.
I have three questions for you:
1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command:
###
mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz
recon-all -s SUBJECT_name -autorecon-all
###
How can I extract the required binary image?
2 - Is it possible to comput only hippocampus region (to reduce the processing time)?
3 - Is it possible to give as input only an ristrected region of the subject's head?
Best regards
Andre Tateo